Straw incorporation is an effective measure for increasing soil organic carbon (SOC) thereby improving soil quality and crop productivity. However, quantitative assessments of the transformation and distribution of exogenous carbon (C) in soil aggregates under various field fertilization practices have been lacking. In this study, we collected topsoil samples (0–20 cm) from three fertilization treatments (no fertilization control, CK; inorganic fertilizer, IF; inorganic fertilizer plus manure, IFM) at a 29-year long-term Mollisol experiment in Northeast China. We then mixed the soil samples with ¹³C-labeled maize straw (δ¹³C = 246.9‰), referred as CKS, IFS, and IFMS, and incubated them in-situ for 360 days. Initial and incubated soil samples were separated into four aggregate fractions (> 2, 1–2, 0.25–1, and < 0.25 mm) using the dry-sieving method, which counted 18%, 17%, 45%, and 21% (averages from the three initial soil samples), respectively. Organic C content was highest in 0.25–1 mm aggregate (6.9–9.6 g kg⁻¹) prior to incubation, followed by > 2 mm aggregates (2.2–5.8 g kg⁻¹), 1–2 mm aggregates (2.4–4.6 g kg⁻¹), and < 0.25 mm aggregates (3.3–4.5 g kg⁻¹). After 360-day incubation with straw incorporation, organic C content was 2.3–4.5 g kg⁻¹, 2.9–5.0 g kg⁻¹, 7.2–11 g kg⁻¹ and 1.8–3.0 g kg⁻¹ in > 2, 1–2, 0.25–1, and < 0.25 mm aggregates, respectively, with the highest in the IFMS treatment. Straw-derived C content was 0.02–0.05 g kg⁻¹, 0.03–0.04 g kg⁻¹, 0.11–0.13 g kg⁻¹, and 0.05–0.10 g kg⁻¹ in > 2, 1–2, 0.25–1, and < 0.25 mm aggregates, respectively. The relative distribution of straw-derived C was highest (40–49%) in 0.25–1 mm aggregate, followed by < 0.25 mm aggregates (21–31%), 1–2 mm aggregates (13–15%), and > 2 mm aggregates (9.4–16%). During the incubation, the relative distribution of straw-derived C exhibited a decrease in > 2 mm and 1–2 mm aggregates, but an increase in the < 0.25 mm aggregate. At the end of incubation, the relative distribution of straw-derived C showed a decrease in the 0.25–1 mm aggregate but an increase in the < 0.25 mm aggregate under the IFMS treatment. This study indicates that more straw-derived C would be accumulated in smaller aggregates over longer period in Mollisols, and combined inorganic and organic fertilization is an effective measure for C sequestration in Northeast China.